The energy minimization calculations on various compounds of biological interest have given insight into their behavior and clues to the possible pharmacophores. Cluster analysis on the retinal isomers show three categories due to energy and conformational variations, which are being related to biological behavior. The four possible conformations of cyclophosphoramide have a stability order in which chair conformations are more stable than boat conformations and the oxygen atom in the equatorial plane increases the stability over that compound in which the oxygen atom is in the axial position. The inhibition of aldose reductase by flavonoids and related compounds is being extended to include the chromon-2-carboxylic acids. It turns out that the most stable form of these molecules is a planar one, contrary to expectations.